Course Introduction
Bioorganic Chemistry
Final Test Solutions
Bioorganic Chemistry explores the intersection of organic chemistry and biochemistry, focusing on the chemical processes and molecular structures underlying biological systems. The course covers the design, synthesis, and function of biomolecules such as proteins, nucleic acids, carbohydrates, and lipids, as well as enzyme mechanisms and cofactors. Students gain an understanding of how organic reactions drive biological processes and how chemical principles are applied in drug design, biotechnology, and the development of molecular probes for studying biological systems. Emphasizing both theory and practical applications, this course equips students with a comprehensive foundation for advanced studies in chemistry, biology, and related fields.
Recommended Textbook
Biochemistry 7th Edition by Mary K. Campbell
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2
Chapter 1: Biochemistry and the Organization of Cells
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Sample Questions
Q1) Which of these kingdoms includes only prokaryotic organisms?
A) Animals
B) Fungi
C) Monera
D) Plants
E) Protista
Answer: C
Q2) How do the molecules that play a role in living cells compare to those encountered in organic chemistry?
A) They are the same, just operating in a different context.
B) Biological molecules are organic molecules, but the similarity ends there.
C) Biological molecules aren't similar to organic molecules at all.
D) Biology isn't based on molecules at all, but a "vital force".
Answer: A
Q3) The mitochondrial matrix
A) is the location of enzymes needed for oxidation reactions
B) contains an array of microtubules
C) is part of the endoplasmic reticulum
D) lies between the inner and outer mitochondrial membrane
Answer: A
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Chapter 2: Water: The Solvent for Biochemical Reactions
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Q1) Hydrogen bonds
A) play an important role in the solvent properties of water
B) are not involved in protein structure
C) play a role in the properties of DNA, but not of RNA
D) give water a lower boiling point than expected
Answer: A
Q2) An ammonia buffer contains NH<sub>3</sub>:NH<sub>4</sub><sup>+</sup> in a ratio of 0.4 moles:0.6 moles (pK = 9.75).What will be the pH if you add 0.01 moles of HCl to this buffer?
A) 8.98
B) 9.04
C) 9.25
D) 9.46
E) 9.52
Answer: A
Q3) Hydrogen bonds can only form when the hydrogen atom is involved in a polar bond.
A)True
B)False
Answer: True
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4
Chapter 3: Amino Acids and Peptides
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Sample Questions
Q1) The amino acids which occur in proteins
A) are all of the L- form.
B) are all of the D- form.
C) can be either the L- or D- form.
D) do not have L- and D- forms.
Answer: A
Q2) Which of the following has no L or D configuration?
A) Glyceraldehyde
B) Proline
C) Glycine
D) All of these have an L or D configuration
Answer: C
Q3) This amino acid displays a free amino group in the peptide ALA-GLN-ARG-SER-HIS:
A) ALA
B) GLN
C) SER
D) HIS
Answer: A
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Chapter 4: The Three-Dimensional Structure of Proteins
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Sample Questions
Q1) Domains are
A) independently folded regions of proteins
B) the a-helical portions of proteins
C) the b-pleated regions of proteins
D) all of the above
Q2) Generally speaking,this type of protein is water-soluble:
A) Fibrous.
B) Globular.
C) Both fibrous and globular proteins are usually water-soluble.
D) Neither fibrous nor globular proteins are usually water-soluble.
E) You cannot generalize about the solubility of fibrous or globular proteins.
Q3) Heme would best be described as a
A) motif.
B) domain.
C) prosthetic group.
D) helix.
Q4) A single amino substitution can give rise to a malfunctioning protein.
A)True
B)False
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Chapter 5: Protein Purification and Characterization Techniques
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Q1) Which of the following is not an example of column chromatography?
A) ammonium sulfate fractionation
B) ion-exchange separation
C) HPLC
D) affinity separation
Q2) Elution of proteins by means of a pH gradient would work best with this type of column:
A) Gel filtration
B) Affinity chromatography
C) Cation exchange
D) Anion exchange
E) Cation or anion exchange
Q3) The isoelectric point is
A) the pH at which a substance has no net charge
B) the pH at which a substance has a net positive charge
C) the pH at which a substance has a net negative charge
D) the pH at which a substance has no charge groups of any kind
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Page 7
Chapter 6: The Behavior of Proteins: Enzymes
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Sample Questions
Q1) If an inhibitor changes the slope of the Lineweaver-Burk graph,but not the y-intercept,it is this type of inhibition:
A) Competitive.
B) Non-competitive.
C) Mixed Inhibition (uncompetitive inhibition).
D) You cannot tell from the data given.
E) More than one answer is correct.
Q2) Which of the following describes the unique importance of protein Kinase Mæ (PKMæ)?
A) It is a protein kinase
B) It uses ATP to phosphorylate a substrate
C) It is an allosteric enzyme
D) It has been implicated in the formation of long-term memories
Q3) When an enzyme is saturated with substrates,
A) it will display zero-order kinetics.
B) it will display first-order kinetics.
C) it will display second-order kinetics.
D) it will denature and cease to function.
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Chapter 7: The Behavior of Proteins: Enzymes, Mechanisms, and Control
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Q1) Which of the following can function as coenzymes?
A) lead ion, biotin, and lipoic acid.
B) copper ion, p-hydroxymercuribenzoate, diisopropylphophofluoridate.
C) zinc ion, pyridoxal phosphate, and nicotinamide adenine nucleotides.
D) lead ion, p-hydroxymercuribenzoate, diisopropylphophofluoridate.
Q2) Which of the following is true?
A) Allosteric enzymes are rarely important in the regulation of metabolic pathways.
B) Michaelis-Menten kinetics describe the reactions of allosteric enzymes
C) Allosteric enzymes have a hyperbolic plot of reaction rate vs. substrate concentration
D) none of these is true
Q3) Which of the following best describes negative cooperativity?
A) Binding of one substrate molecule prevents the enzyme from working at all.
B) Binding of one substrate molecule inhibits the binding of a second substrate.
C) Binding of one substrate molecule enhances the binding of a second substrate.
D) Binding of one substrate molecule inhibits the binding of other effectors.
Q4) The term K<sub>0.5</sub> is analogous to the K<sub>M</sub>
A)True
B)False
Page 9
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Chapter 8: Lipids and Proteins Are Associated in Biological Membranes
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Sample Questions
Q1) Which of the following is not a lipid-soluble vitamin?
A) Ascorbic Acid
B) Cholicalciferol
C) Vitamin K
D) Retinol
E) Tocopherol
Q2) Which of the following is not true?
A) Plant oils are favored in the diet because they generally contain more unsaturated fats than found in animal fats.
B) Unsaturated fatty acids are healthier for humans than saturated ones
C) Heart disease can be correlated with diets high in saturated fatty acids
D) Unsaturated fatty acids lead to higher levels of LDL than saturated fatty acids do
Q3) Which of the following is a metabolic precursor of prostaglandins & leukotrienes?
A) vitamin A
B) arachidonic acid.
C) sphingomyelin.
D) cholesterol.
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Page 10
Chapter 9: Nucleic Acids: How Structure Conveys
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Q1) Which of the following characteristics is associated with the B form of DNA?
A) the sugars are located in the interior of the double helix
B) the distance between base pairs along the axis of the helix is 8 Å
C) the major and minor grooves are readily apparent
D) the planes of the bases make about a 20 degree angle with the helix axis
Q2) Which of the following best describes the structure of a nucleosome?
A) DNA wrapped around an octomer containing two each of H2A, H2B, H3, and H4 with H1 on the outside.
B) DNA wrapped around an octomer of H1 with H2A,B, H3 & H4 on the outside.
C) DNA wrapped around a octomer of either H2A/H2B or H3/H4 with H1 on the outside.
D) DNA wrapped around a tetramer of either H2A/H2B or H3/H4 with H1 on the outside.
Q3) The following types of RNA are common to all organisms,except:
A) mRNA
B) rRNA
C) snRNA
D) tRNA
E) All types are found in all organisms.
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Page 11
Chapter 10: Biosynthesis of Nucleic Acids: Replication
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Q1) Which of the following characteristics is not associated with A) it synthesizes the RNA primer in DNA replication
B) it synthesizes a primer with a free 3'-OH end
C) it is essential for DNA replication
D) it is essential for RNA replication
E) coli primase?
Q2) One major difficulty in replicating linear DNA molecules is replacing the segment of DNA occupied by the RNA primer on the telomeres at the ends of the DNA.
A)True
B)False
Q3) In the original Central Dogma of biology,the ordinary flow of genetic information is:
A) DNA RNA Protein
B) RNA DNA Protein
C) Protein RNA DNA
D) DNA Protein RNA.
E) None of these
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12
Chapter 11: Transcription of the Genetic Code: Biosynthesis of Rna
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Sample Questions
Q1) Which of following statements concerning RNA transcription is false?
A) The DNA strands become separated during synthesis.
B) Synthesis of RNA is as accurate as synthesis of DNA
C) The template strand is read in the 3' 5' direction.
D) All 4 ribonucleotides are required.
Q2) All of the following apply to attenuation mechanisms,except:
A) They are used most often for operons for amino acid synthesis.
B) They involve the synthesis of proteins in the regulation of RNA synthesis.
C) The rate of RNA synthesis is regulated by the conformation of the protein being synthesized.
D) They require the presence of partially completed mRNA molecules.
E) All of these apply to attenuation mechanisms.
Q3) At what point does the sigma (s) subunit of RNA polymerase released from the core enzyme?
A) Prior to the incorporation of any nucleotides into an RNA strand.
B) After transcription begins and about 10 nucleotides have been added to the RNA chain.
C) Just prior to chain termination.
D) Never; it is an intrinsic part of the core enzyme.
Page 13
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Chapter 12: Protein Synthesis: Translation of the Genetic Message
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Q1) Specificity of aminoacyl-tRNA synthetases is always based on the anticodon.
A)True
B)False
Q2) At which position on tRNA is the wobble base of the triplet anticodon?
A) 1<sup>st</sup> position (5' letter)
B) 2<sup>nd</sup> position
C) 3<sup>rd</sup> position (3' letter)
D) Wobble can occur at any position.
Q3) The template for protein synthesis is:
A) a mRNA strand
B) the DNA coding strand
C) the DNA template strand
D) a protein primer
E) none of these
Q4) A polysome is
A) a complex consisting of one mRNA to which several ribosomes are attached
B) a polypeptide chain in the process of being formed
C) an intermediate stage in the self-assembly of ribosomes
D) an aggregate of ribosomal proteins
Page 14
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Chapter 13: Nucleic Acid Biotechnology Techniques
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Sample Questions
Q1) Fluorescence works because the fluorescent molecule
A) absorbs light at one wavelength and emits light at a longer wavelength.
B) absorbs light at one wavelength and emits light at a shorter wavelength.
C) absorbs light at one wavelength and emits light at the same wavelength.
D) absorbs light at many wavelengths and emits light at many wavelengths.
Q2) Multi-cloning sites ("poly-linkers") in most commercially available plasmids offer all the following advantages over the earlier plasmids used in genetic recombination except:
A) They can be used with a wide variety of restriction enzymes.
B) They assure that only the desired DNA will be inserted into the plasmid.
C) They enable easy control of the direction of insertion of the gene of interest.
D) They are usually adjacent to any necessary promoters for gene expression.
E) All of these are advantages.
Q3) Genetic engineering which recombines DNA from different species is
A) a molecular extension of traditional cross-breeding methods.
B) only possible with plants.
C) only possible with animals.
D) only possible with bacteria.
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Page 15
Chapter 14: Viruses, Cancer, and Immunology
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Q1) A virus life cycle that involves the incorporation of the viral DNA into the host chromosome is
A) lysogeny.
B) lytic.
C) oncogenic.
D) non-existent.
Q2) Antibodies have two binding sites to react with antigens.
A)True
B)False
Q3) Which of the following best describes the function of reverse transcriptase?
A) It's involved in viral attachment to a host cell.
B) It uses an RNA template to make a double-stranded DNA.
C) It uses DNA to synthesize an RNA in the 3' 5' direction.
D) It joins the gene segments that code for antibodies.
Q4) Hybridomas,which produce monoclonal antibodies,are made by fusing cells of the immune system with A) cancerous cells.
B) viruses.
C) bacterial cells.
D) ribosomes.
Page 16
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Chapter 15: The Importance of Energy Changes and
Electron Transfer in Metabolism
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Q1) An example of an activation step in metabolism is
A) the hydrolysis of a triacylglycerol.
B) the cis-trans isomerization of retinal.
C) the formation of an acyl derivative of coenzyme A
D) the formation of the peptide bond.
Q2) Many cells oxidize fatty acids to produce ATP.If no ATP were produced,the DG° of this process would be
A) unchanged
B) a larger positive number
C) a larger negative number
D) impossible to determine
Q3) What happens to the entropy when ATP is hydrolysed to ADP?
A) Entropy increases
B) Entropy decreases.
C) Entropy doesn't change.
D) ATP has no entropy.
Q4) In general,catabolism
A) releases energy.
B) absorbs energy.
C) neither absorbs nor releases energy.
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Chapter 16: Carbohydrates
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Q1) Maltose is composed of the following simple sugars:
A) galactose only
B) glucose only
C) fructose only
D) galactose and glucose
E) glucose and fructose
F) galactose and fructose
Q2) Cartilage and mucous are both slippery because:
A) Short polymers comprise these compounds.
B) The charge repulsion between the many acid groups in these polymers.
C) The sticky nature of sugars.
D) Both charge repulsion of acidic groups and the sticky nature of sugars.
E) All of these
Q3) Insoluble fiber in the diet is better at binding toxic substances than soluble fiber.
A)True
B)False
Q4) Plant starch includes amylopectin and cellulose
A)True
B)False
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Chapter 17: Glycolysis
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Q1) In the conversion of glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate
A) an alcohol group is phosphorylated.
B) an alcohol is oxidized to an aldehyde.
C) an alcohol is oxidized to a carboxylic acid.
D) an aldehyde is oxidized to a carboxylic acid.
Q2) How many enzymes of glycolysis are control points for the pathway?
A) 1
B) 2
C) 3
D) 4
E) All the enzymes serve as control points.
Q3) During anaerobic metabolism in yeast,the carbons of glucose end up in A) CO<sub>2</sub>.
B) ethanol.
C) lactic acid.
D) both CO<sub>2</sub> and ethanol.
E) all of these
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Chapter 18: Storage Mechanisms and Control in Carbohydrate Metabolism
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Q1) Which of the following mechanisms can be used to regulate metabolic pathways?
A) Allosteric activators and inhibitors.
B) Covalent modifications of enzymes.
C) Use of separate enzymes at a given point in the forward and backward pathways.
D) Regulation of the genes for the enzymes used in the pathway.
E) All of these are used to regulate metabolism.
Q2) Which of the following is not a control mechanism for glycogen phosphorylase?
A) Covalent modification.
B) Inhibition by glucose.
C) Subunit association and dissociation.
D) Allosteric stimulation by AMP.
E) All of these mechanisms regulate the activity of glycogen synthase.
Q3) Which of the following statements concerning the initial phase of the pentose phosphate pathway is false?
A) A CO<sub>2</sub> molecule is released from glucose.
B) Two molecules of NADPH are produced per glucose.
C) Ribulose-5-phosphate is produced by an oxidative decarboxylation of 6-phosphogluconate.
D) The process reduces glucose-6-phosphate.
Page 20
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Chapter 19: The Citric Acid Cycle
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Q1) In muscle cells,the following reaction proceeds as written,i.e.,from left to right,despite having DG°' » +30 kJ/mol.How can this occur? malate + NAD<sup>+</sup> oxaloacetate + NADH + H<sup>+</sup>
A) It is obviously thermodynamically favored under standard conditions.
B) In the cell, it is kinetically favored, even though it's thermodynamically unfavored.
C) The concentration of malate must be higher than oxaloacetate for this reaction to occur in the cell.
D) [H<sup>+</sup>] must be higher in muscle than under standard conditions, thus altering DG°' to DG°.
Q2) The conversion of citrate to isocitrate is remarkable because
A) it is a condensation reaction.
B) a chiral center is introduced in a molecule that did not have one previously.
C) a dehydration reaction is involved.
D) the enzyme that catalyzes it has very little specificity.
Q3) The citric acid cycle is the only metabolic pathway that can be used both as an anabolic and as a catabolic pathway.
A)True
B)False
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21
Chapter 20: Electron Transport and Oxidative
Phosphorylation
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Q1) The only complex which actually uses molecular oxygen is
A) Complex I.
B) Complex II.
C) Complex III.
D) Complex IV.
E) It is not known where oxygen is used.
Q2) Brown adipose tissue is partially responsible for generating heat in the young human body.
A)True
B)False
Q3) The only reaction which actually uses molecular oxygen is
A) Cytochrome C oxidase.
B) NADH-CoQ reductase.
C) succinate-CoQ reductase.
D) Cytochrome A oxidase.
E) Cytochrome bc<sub>1</sub> complex.
Q4) Transition metals are especially important in electron transport,since they have variable oxidation states.
A)True
B)False
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Chapter 21: Lipid Metabolism
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Q1) Since acetyl-CoA carboxylase is key to the synthesis of fatty acids,inhibitors of this enzyme may be useful for weight loss or treatment of obesity.
A)True
B)False
Q2) Which of the following best describes carnitine?
A) It transports fatty acids across the inner mitochondrial membrane for breakdown.
B) It transports acetyl-CoA to the cytosol for fatty acid synthesis.
C) It's a precursor of cholesterol.
D) It carries growing acyl chains during fatty acid synthesis.
Q3) How many NAD<sup>+</sup> are reduced in the degradation of palmitoyl-CoA to form eight molecules of acetyl-CoA?
A) 1
B) 7
C) 8
D) 14
E) 16
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Chapter 22: Photosynthesis
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Q1) Anaerobic,photosynthetic bacteria differ from green plants in that they only have one type of chlorophyll.
A)True
B)False
Q2) The light reactions drive the redox process that involves the following pairs of reactants/products
A) H<sub>2</sub>O/O<sub>2</sub> and NADP<sup>+</sup>/NADPH
B) H<sub>2</sub>O/O<sub>2</sub> and NADH/NAD<sup>+</sup>
C) O<sub>2</sub>/H<sub>2</sub>O and NADPH/NADP<sup>+</sup>
D) H<sub>2</sub>O/O<sub>2</sub> and FAD/FADH<sub>2</sub>
Q3) During Z-scheme photosynthesis,ferredoxin oxidizes NADPH.
A)True
B)False
Q4) In plants that use the C<sub>4</sub> pathway there is less likelihood for the occurrence of which process compared to plants that rely exclusively on the Calvin cycle?
A) gluconeogenesis
B) photorespiration
C) the pentose phosphate pathway
D) lipid anabolism
Page 24
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Chapter 23: The Metabolism of Nitrogen
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Q1) Isoleucine,leucine and valine are all formed from the same amino acid root,aspartic acid.
A)True
B)False
Q2) How many ATP equivalents are required to produce one molecule of urea from ammonia and aspartate?
A) 1
B) 2
C) 3
D) 4
E) 6
Q3) A coenzyme frequently encountered in transamination reactions is A) tetrahydrofolate.
B) pyridoxal phosphate.
C) thiamine pyrophosphate.
D) biotin.
Q4) The synthesis of amino acids occurs in about 5 or 6 related families of amino acids. A)True B)False
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Chapter 24: Integration of Metabolism: Cellular Signaling
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Q1) Amino acid and protein hormones usually act by binding to a receptor on the cell surface.
A)True
B)False
Q2) Which of the following fats are linked with high cholesterol and heart disease?
A) saturated fats
B) monounsaturated fats
C) polyunsaturated fats
D) all fats, regardless of saturation
Q3) Regulatory cascades have what advantage over direct action by the signal molecule?
A) Amplification.
B) Fine tuning of regulatory effects.
C) Coordinated response among multiple systems.
D) All of these
Q4) Glycogen metabolism is influenced by
A) phosphorylase kinase
B) phosphoprotein phosphatase
C) epinephrine
D) all of these
26
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